[Chimera-users] turning kdssp off

[Elaine Meng]

Hi Matt,
The slowness is probably the “chemical perception” rather than the secondary structure stuff.  

Although Chimera does not have an option to turn this off, ChimeraX does; see ChimeraX command “open” with “atomic false” option:
<http://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#local>

ChimeraX is generally better (faster) with large data, and it also has the “molmap” command for transforming atomic coordinates to density:
<http://rbvi.ucsf.edu/chimerax/docs/user/commands/molmap.html>

Like Chimera, ChimeraX is free for noncommercial use.
<http://www.rbvi.ucsf.edu/chimerax/>
<http://www.rbvi.ucsf.edu/chimerax/download.html>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Jul 16, 2018, at 9:47 AM, Mateusz Sikora <masikora at biophys.mpg.de> wrote:
> 
> Dear Chimera users,
> is there any way to turn the secondary structure assignment (kdssp) off?
> 
> I am transforming a set of coordinates from a MD trajectory into
> electron density. I collapsed many frames of the trajectory into a
> single file, meaning there are many unphysical overlaps (I only care
> about the density). Problem is, that the PDB file I am opening is rather
> large (couple of millions of atoms) and kdssp gets absolutely stuck on it.
> 
> I would appreciate some help.
> Best regards,
> Matt